This is just my personal opinion on how I prefered that the main story ended… disagree/agree with it at your wil. This is not a post meant to argue with other posters as to “who has the better idea of how the story should’ve ended”, but rather a random thought I had while replaying the whole story recently.
-The vault hunters head to the Cathedral of the Twins and faces Troy as usual.
-Troy is defeated but doesn’t dies right away. He gets angry for losing the fight against the vault hunter(s), mocks them and then he phaselocks the vault hunter(s) and tells Tyreen to hurry up release the Destroyer.
-The Destroyer is released, Troy uses his Phaselock powers to quickly slam the vault hunter(s) in the ground, then he runs towards Tyreen, and as they try to absorb him, things doesn’t work out like they were hoping it would… the Destroyer ends up overpowering them, resulting in both the twins being now merged to the Destroyer, forming a creature named The Chimera (the mythological Chimera was a creature composed of multiple creatures and was the son of Typhoon), keeping the greek naming theme going as the final boss of the base game, with the irony of Tyreen, who wanted to be a god and referring to her brother as a “parasite” because he was born conjoined to her, is now merged with her brother once more, but in the body of a creature that is much more powerful to her, as a mere “parasite” to this creature.
-The whole Nekrotafeyo arc is now saved for a DLC content, where we get to meet Typhon DeLeon, where he gives us more insight about the vaults, the Eridians, that the twins were his kids all along, etc… The Nekrotafeyo arc would play mostly the same, with some minor modifications, obviously and with Typhon actually surving in the end, as I think killing him was a waste of potential for an interesting character.